MatSAM: a Matlab implementation for Significance Analysis of Microarrays

Abstract

Microarray experiments enable the simultaneous measure of expression levels of large amount of genes and have many applications. A widespread one is finding set of genes that are differentially expressed. Significance Analysis of Microarrays (SAM) helps to produce those sets using multiple testing techniques. There is unfortunately not yet a public tool enabling to do SAM using the Matlab platform. We here define MatSAM, a SAM implementation in Matlab, and show that it yields results of high confidence comparatively to those obtained by putative tools available in the R programming environment. MatSAM can be used in conjunction with Matlab Bioinformatics toolbox to perform further analysis.